ZerNet: Convolutional Neural Networks on Arbitrary Surfaces via Zernike Local Tangent Space Estimation

In this paper, we propose a novel formulation to extend CNNs to two-dimensional (2D) manifolds using orthogonal basis functions, called Zernike polynomials. In many areas, geometric features play a key role in understanding scientific phenomena. Thus, an ability to codify geometric features into a mathematical quantity can be critical. Recently, convolutional neural networks (CNNs) have demonstrated the promising capability of extracting and codifying features from visual information. However, the progress has been concentrated in computer vision applications where there exists an inherent grid-like structure. In contrast, many geometry processing problems are defined on curved surfaces, and the generalization of CNNs is not quite trivial. The difficulties are rooted in the lack of key ingredients such as the canonical grid-like representation, the notion of consistent orientation, and a compatible local topology across the domain. In this paper, we prove that the convolution of two functions can be represented as a simple dot product between Zernike polynomial coefficients; and the rotation of a convolution kernel is essentially a set of 2-by-2 rotation matrices applied to the coefficients. As such, the key contribution of this work resides in a concise but rigorous mathematical generalization of the CNN building blocks

Pycortex: an interactive surface visualizer for fMRI.

Surface visualizations of fMRI provide a comprehensive view of cortical activity. However, surface visualizations are difficult to generate and most common visualization techniques rely on unnecessary interpolation which limits the fidelity of the resulting maps. Furthermore, it is difficult to understand the relationship between flattened cortical surfaces and the underlying 3D anatomy using tools available currently. To address these problems we have developed pycortex, a Python toolbox for interactive surface mapping and visualization. Pycortex exploits the power of modern graphics cards to sample volumetric data on a per-pixel basis, allowing dense and accurate mapping of the voxel grid across the surface. Anatomical and functional information can be projected onto the cortical surface. The surface can be inflated and flattened interactively, aiding interpretation of the correspondence between the anatomical surface and the flattened cortical sheet. The output of pycortex can be viewed using WebGL, a technology compatible with modern web browsers. This allows complex fMRI surface maps to be distributed broadly online without requiring installation of complex software

ENABLING TECHNIQUES FOR EXPRESSIVE FLOW FIELD VISUALIZATION AND EXPLORATION

Flow visualization plays an important role in many scientific and engineering disciplines such as climate modeling, turbulent combustion, and automobile design. The most common method for flow visualization is to display integral flow lines such as streamlines computed from particle tracing. Effective streamline visualization should capture flow patterns and display them with appropriate density, so that critical flow information can be visually acquired. In this dissertation, we present several approaches that facilitate expressive flow field visualization and exploration. First, we design a unified information-theoretic framework to model streamline selection and viewpoint selection as symmetric problems. Two interrelated information channels are constructed between a pool of candidate streamlines and a set of sample viewpoints. Based on these information channels, we define streamline information and viewpoint information to select best streamlines and viewpoints, respectively. Second, we present a focus+context framework to magnify small features and reduce occlusion around them while compacting the context region in a full view. This framework parititions the volume into blocks and deforms them to guide streamline repositioning. The desired deformation is formulated into energy terms and achieved by minimizing the energy function. Third, measuring the similarity of integral curves is fundamental to many tasks such as feature detection, pattern querying, streamline clustering and hierarchical exploration. We introduce FlowString that extracts shape invariant features from streamlines to form an alphabet of characters, and encodes each streamline into a string. The similarity of two streamline segments then becomes a specially designed edit distance between two strings. Leveraging the suffix tree, FlowString provides a string-based method for exploratory streamline analysis and visualization. A universal alphabet is learned from multiple data sets to capture basic flow patterns that exist in a variety of flow fields. This allows easy comparison and efficient query across data sets. Fourth, for exploration of vascular data sets, which contain a series of vector fields together with multiple scalar fields, we design a web-based approach for users to investigate the relationship among different properties guided by histograms. The vessel structure is mapped from the 3D volume space to a 2D graph, which allow more efficient interaction and effective visualization on websites. A segmentation scheme is proposed to divide the vessel structure based on a user specified property to further explore the distribution of that property over space

Conceptual framework of a novel hybrid methodology between computational fluid dynamics and data mining techniques for medical dataset application

This thesis proposes a novel hybrid methodology that couples computational fluid dynamic (CFD) and data mining (DM) techniques that is applied to a multi-dimensional medical dataset in order to study potential disease development statistically. This approach allows an alternate solution for the present tedious and rigorous CFD methodology being currently adopted to study the influence of geometric parameters on hemodynamics in the human abdominal aortic aneurysm. This approach is seen as a “marriage” between medicine and computer domains

A (Near) Real-Time Simulation Method of Aneurysm Coil Embolization

International audienceA (Near) Real-Time Simulation Method of Aneurysm Coil Embolizatio

DeepVox and SAVE-CT: a contrast- and dose-independent 3D deep learning approach for thoracic aorta segmentation and aneurysm prediction using computed tomography scans

Thoracic aortic aneurysm (TAA) is a fatal disease which potentially leads to dissection or rupture through progressive enlargement of the aorta. It is usually asymptomatic and screening recommendation are limited. The gold-standard evaluation is performed by computed tomography angiography (CTA) and radiologists time-consuming assessment. Scans for other indications could help on this screening, however if acquired without contrast enhancement or with low dose protocol, it can make the clinical evaluation difficult, besides increasing the scans quantity for the radiologists. In this study, it was selected 587 unique CT scans including control and TAA patients, acquired with low and standard dose protocols, with or without contrast enhancement. A novel segmentation model, DeepVox, exhibited dice score coefficients of 0.932 and 0.897 for development and test sets, respectively, with faster training speed in comparison to models reported in the literature. The novel TAA classification model, SAVE-CT, presented accuracies of 0.930 and 0.922 for development and test sets, respectively, using only the binary segmentation mask from DeepVox as input, without hand-engineered features. These two models together are a potential approach for TAA screening, as they can handle variable number of slices as input, handling thoracic and thoracoabdominal sequences, in a fully automated contrast- and dose-independent evaluation. This may assist to decrease TAA mortality and prioritize the evaluation queue of patients for radiologists.Comment: 23 pages, 4 figures, 7 table